• Ocean and Polar Research
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• v.25 no.4
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• pp.607-615
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• 2003

Many organisms are known to survive in icy environments. These include both over wintering terrestrial insects and plants as well the marine fish inhabiting high latitudes. The adaptation of these organisms is both a fascinating and important topic in biology. Marine teleosts in particular, can encounter ice-laden seawater that is approximately $1^{\circ}C$ colder than the colligative freezing point of their body fluids. These animals produce a unique group of proteins, the antifreeze proteins (AFPs) or antifreeze glycoproteins (AFGPs) that absorb the ice nuclei and prevent ice crystal growth. Presently, there are at least four different AFP types and one AFGP type that are isolated from a wide variety of fish. Despite their functional similarity, there is no apparent common protein homology or ice-binding motifs among these proteins, except that the surface-surface complementarity between the protein and ice are important for binding. The remarkable diversity of these proteins and their odd phylogenetic distribution would suggest that these proteins might have evolved recently in response to sea level glaciations just 1-2 million years ago in the northern hemisphere and 10-30 million years ago around Antarctica. Winter flounder, Pleuronectes americanus, has been used as a popular model to study the regulation of AFP gene expression. It has a built-in annual cycle of AFP expression controlled negatively by the growth hormone. The signal transduction pathways, transcription factors and promoter elements involved in this process have been studied in our laboratory and these studies will be presented.

• ALGAE
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• v.35 no.2
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• pp.145-155
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• 2020

Specimens of red algae corresponding to the peyssonnelioid genus Sonderophycus were collected at Kure Atoll, Hawai'i, at a depth range of 88-94 m depth during mesophotic surveys of the Papahānaumokuākea Marine National Monument, Hawaiian Islands, and were analyzed using morphological and molecular approaches. Analyses of mitochondrial cytochrome oxidase subunit 1 and chloroplast rbcL DNA sequences demonstrated that the Hawaiian specimens were identical to one another yet distinct from the three other species currently recognized within the genus (S. capensis [Montagne] M. J. Wynne, S. coriaceus [Womersley & Sinkora] M. J. Wynne, and S. fervens Dixon), as well as the likely congener, Peyssonnelia caulifera Okamura, and are proposed here as a new species: Sonderophycus copusii A. R. Sherwood. Sonderophycus copusii is morphologically distinct from other members of the genus by the following combination of characters: the presence of occasional secondary perithallial growth, emergence of rhizoids from the hypobasal cuticle at a strongly acute angle, a lack of horizontally directed filaments in the lower perithallus, and the lack of a stipe. This is the first record of the genus Sonderophycus in the Hawaiian Islands. Sonderophycus copusii was documented as a dominant member of the algal community at Kure Atoll, and thus may play a significant ecological role in the deep-water benthic community of Kure Atoll, along the lines of reports of deep water peyssonnelioid beds in the Mediterranean, Red Sea, and Caribbean. This study further highlights the unexplored diversity of the Peyssonneliales in Hawai'i, and emphasizes more generally the degree of as yet undiscovered biodiversity of algae at mesophotic depths.

• Mycobiology
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• v.47 no.4
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• pp.368-377
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• 2019

The genus Macrolepiota (Agaricales, Basidiomycota) is easy to recognize at the genus level because of big, fleshy basidiocarps with squamules covering the pileus; a single or double annulus; and big, thick-walled basidiospores with a germ pore. However, morphological identification is often unreliable in Macrolepiota due to similar morphological features among species. Due to the uncertainty of previous morphological identification in the genus Macrolepiota, it is necessary to re-examine Korean Macrolepiota using molecular data. We reexamined 34 Macrolepiota specimens collected from 2012 to 2018 in Korea using a reverse taxonomic approach, whereby species identification was first done based on the internal transcribed spacer (ITS) region analysis, followed by morphological confirmation. We identified the presence of four species: M. detersa, M. mastoidea, M. procera, and M. umbonata sp. nov. Two species (M. detersa and M. mastoidea) were previously unrecorded from Korea and M. umbonata is a new species. Detailed descriptions of all four species and taxonomic key are provided in this study. Macrolepiota procera and M. umbonata are distributed through the country, but M. detersa and M. mastoidea are distributed only in limited areas. According to our results, the combination of ITS locus and morphology proved to be a robust approach to evaluate the taxonomic status of Macrolepiota species in Korea. Additional surveys are needed to verify the species diversity and clarify their geographic distribution.

• Restorative Dentistry and Endodontics
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• v.19 no.2
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• pp.485-498
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• 1994

Porphyromonas endodontalis is a black-pigmented anaerobic Gram-negative rod which is associated with endodontal infections and this microorganism possesses a potential for pathogenicity. The purpose of this study was to compare the membrane components of Porphyromonas endodontalis and Porphyromonas gingivalis and to study the immune reaction patterns of Porphyromonas endodontalis with patients with periapical lesion. Porphyromonas endodontalis (ATCC 35406), Porphyromonas gingivals serotypea (381), serotype b(W50), serotype c(A7A1-28) were cultured in anaerobic condition. Rabbit antisera were prepared by intravenous injection of formalized whole cells and human sera were obtained from patients and dental students. Indirect immunofluorescence method was used to study on the cross reaction between Porphyromonas endodontalis and Porphyromonas gingivalis serotype a, b, c antigen. Total membrane protein profiles of Porphyromonas endodontalis antigen were studied by sodium dodecyl sulfate polyacrylamide gel electrophoresis and the reactivity of antigenic components of Porphyromonas endodontalis against sera of patients and rabbit anti-Porphyromonas endodontalis antisera were assessed by Immunoblotting method. The following results were obtained : 1. Antigens of Porphyromonas endodontalis has multiple antigenic components, and both patients with periapical lesion and normal healthy individual showed immune response to this. 2. Patients group and healthy individual group showed a diversity of immune reaction pattern but they showed immune response against 43kd protein. 3. Patients with periapical lesion showed more diverse immune response than healthy individual and in some patients, much more bands appeared to lower molecular weight protein. 4. According to indirect immunofluorescence and Immunoblotting study, Porphyromonas endodontalis did not share common antigen with Porphyromonas gingivalis serotype a, b, c.

• Journal of Microbiology and Biotechnology
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• v.18 no.12
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• pp.1966-1974
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• 2008

A typical tropical soil from the northeast of Brazil, where an important terrestrial oil field is located, was accidentally contaminated with a mixture of oil and saline production water. To study the bioremediation potential in this area, molecular methods based on PCR-DGGE were used to determine the diversity of the bacterial communities in bulk and in contaminated soils. Bacterial fingerprints revealed that the bacterial communities were affected by the presence of the mixture of oil and production water, and different profiles were observed when the contaminated soils were compared with the control. Halotolerant strains capable of degrading crude oil were also isolated from enrichment cultures obtained from the contaminated soil samples. Twenty-two strains showing these features were characterized genetically by amplified ribosomal DNA restriction analysis (ARDRA) and phenotypically by their colonial morphology and tolerance to high NaCl concentrations. Fifteen ARDRA groups were formed. Selected strains were analyzed by 16S rDNA sequencing, and Actinobacteria was identified as the main group found. Strains were also tested for their growth capability in the presence of different oil derivatives (hexane, dodecane, hexadecane, diesel, gasoline, toluene, naphthalene, o-xylene, and p-xylene) and different degradation profiles were observed. PCR products were obtained from 12 of the 15 ARDRA representatives when they were screened for the presence of the alkane hydroxylase gene (alkB). Members of the genera Rhodococcus and Gordonia were identified as predominant in the soil studied. These genera are usually implicated in oil degradation processes and, as such, the potential for bioremediation in this area can be considered as feasible.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.437-447
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• 2012

Natural and beneficial associations between plants and bacteria have demonstrated potential commercial application for several agricultural crops. The sunflower has acquired increasing importance in Brazilian agribusiness owing to its agronomic characteristics such as the tolerance to edaphoclimatic variations, resistance to pests and diseases, and adaptation to the implements commonly used for maize and soybean, as well as the versatility of the products and by-products obtained from its cultivation. A study of the cultivable bacteria associated with two sunflower cultivars, using classical microbiological methods, successfully obtained isolates from different plant tissues (roots, stems, florets, and rhizosphere). Out of 57 plant-growth-promoting isolates obtained, 45 were identified at the genus level and phylogenetically positioned based on 16S rRNA gene sequencing: 42 Bacillus (B. subtilis, B. cereus, B. thuringiensis, B. pumilus, B. megaterium, and Bacillus sp.) and 3 Methylobacterium komagatae. Random amplified polymorphic DNA (RAPD) analysis showed a broad diversity among the Bacillus isolates, which clustered into 2 groups with 75% similarity and 13 subgroups with 85% similarity, suggesting that the genetic distance correlated with the source of isolation. The isolates were also analyzed for certain growth-promoting activities. Auxin synthesis was widely distributed among the isolates, with values ranging from 93.34 to 1653.37 ${\mu}M$ auxin per ${\mu}g$ of protein. The phosphate solubilization index ranged from 1.25 to 3.89, and siderophore index varied from 1.15 to 5.25. From a total of 57 isolates, 3 showed an ability to biologically fix atmospheric nitrogen, and 7 showed antagonism against the pathogen Sclerotinia sclerotiorum. The results of biochemical characterization allowed identification of potential candidates for the development of biofertilizers targeted to the sunflower crop.

• Korean Journal of Environmental Biology
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• v.25 no.4
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• pp.356-362
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• 2007

The rhizobacterial diversity associated with 9 native plant species inhabiting coastal sand dunes in Tae-an area, Chungnam Province, was studied using the denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis over three times from October 2003 to March 2004. One dominant band commonly occurred in all of the rhizosphere samples, which was identified as that of Lysobacter enzymogenes. The other common bands included those derived from species of Pseudomonas and Bacillus. It was notable that L. enzymogenes was dominant in all of the 9 plant species and such dominance was consistent throughout the whole sampling period, which confirms the previous study by Lee et al. (2006a). The Bacillus bands were detected in all of the three samplings, and those of Pseudomonas were notable in the samples of December 2003. By the DGGE analysis alone, the significance of Lysobacter to the sand dune plants is not clear. However, considering their presence in healthy plants and the dominance in all plant species, Lysobacter may have positive roles in the survival or growth of the plants in sand dune area.

• The Journal of Korean Society of Virology
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• v.29 no.2
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• pp.65-74
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• 1999

Reovirus was found to inhabit both the respiratory and the enteric tract of human and animals. The genome of reovirus comprises 10 segments of double-stranded RNA, total size 24 kbp. Nine strains of reovirus were isolated from human and field mice in Korea. Aseptically collected sera from human and lung tissues from field mice were used for virus isolation. For serotype determination, hemagglutination inhibition test was used, and three strains were confirmed to type 2 and six strains to type 3. To determine the genomic diversity and molecular phylogeny of reoviruses isolated in Korea, part of S4 genomic segment of reovirus was enzymatically amplified and directly sequenced. In nucleotide level, Apo98-35 strain showed 15.4%, 19.3%, and 14.4% differences compared to type 1 (T1L, Lang), type 2 (T2J), and type 3 reference strains, respectively. In amino acid level, Apo98-35 strain showed 10.5%, 13.7%, and 9.5% differences compared to type 1, type 2, and type 3 reference strains, respectively. Using the maximum parsimony method based on 285 bp spaning region of the S4 genomic segment, phylogenetic analysis indicated that Apo98-35 from Korea formed different phylogenetic branch. Our data obtained by sequence and phylogenetic analyses of reoviruses are consistent with the distinct geographically dependent evolution of reoviruses in Korea.

• Journal of Life Science
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• v.19 no.6
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• pp.693-697
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• 2009

The purpose of the present investigation was to investigate diversity patterns in Mt. Neungdong forested landscape. It was conducted on twelve sloping plots $(100{\times}100 m)$ in the east and west sides of Mt. Neungdong. A total of 2,157 specimins were identified as trees with a diameter at breast height (DBH) ${\geq}$10 em. There were a total of 135 species of 35 families present in both regions of Mt. Neungdong. Least significant differences (LSD) by post hoc analysis revealed that region A had significantly greater densities than region B. Shannon-Wiener functions differed significantly between forests (F=4.12, < 0.05), with region B forest having a significantly higher value (2.118) than region A (1.882). Pinus thunbergii and Quercus aliena were dominant on most plots of both regions, however, the P. densiflora forest of region A was distributed better in the middle plots exposures compared to the opposite ones. Q. aliena, Q. mongolica, and Carpinus laxiflora largely occupied the middle and lower exposures of region B. The spatial distribution in Neungdong's forest was very heterogeneous and reflected by most species as having micro-climate and patchy distributions.

• Molecules and Cells
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• v.39 no.12
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• pp.862-868
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• 2016

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and cross-bred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.